How Can I fix my Myson Economist WM30/40BF Boiler?

We recently sustained some wind damage to the rear of the house. The wind had managed to remove the exterior part of the boiler (Outlet) and part of the flue. The Boiler was still working without these but I turned it off. I replaced the flue and outlet and the boiler won't ignite anymore. The pilot light remains on at all times. Can anyone help. I am freezing. The boiler in question is a MYSON Economist WM30/40BF.